Active maintenance of CD8+ T cell naivety through regulation of global genome architecture

The differentiation of naive CD8+ T lymphocytes into cytotoxic effector and memory CTL results in large-scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organization underpin these transcriptional programs. We use Hi-C to map changes in the spatial organization of long-range genome contacts within naive, effector, and memory virus-specific CD8+ T cells. We observe that the architecture of the naive CD8+ T cell genome is distinct from effector and memory genome configurations, with extensive changes within discrete functional chromatin domains associated with effector/memory differentiation. Deletion of BACH2, or to a lesser extent, reducing SATB1 DNA binding, within naive CD8+ T cells results in a chromatin architecture more reminiscent of effector/memory states. This suggests that key transcription factors within naive CD8+ T cells act to restrain T cell differentiation by actively enforcing a unique naive chromatin state.

Parallel use of human stem cell lung and heart models provide insights for SARS-CoV-2 treatment

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe coronavirus disease 2019 (COVID-19). To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type II (AT2) epithelial cell and cardiac cultures infected with SARS-CoV-2. With CRISPR-Cas9-mediated knockout of ACE2, we demonstrated that angiotensin-converting enzyme 2 (ACE2) was essential for SARS-CoV-2 infection of both cell types but that further processing in lung cells required TMPRSS2, while cardiac cells required the endosomal pathway. Host responses were significantly different; transcriptome profiling and phosphoproteomics responses depended strongly on the cell type. We identified several antiviral compounds with distinct antiviral and toxicity profiles in lung AT2 and cardiac cells, highlighting the importance of using several relevant cell types for evaluation of antiviral drugs. Our data provide new insights into rational drug combinations for effective treatment of a virus that affects multiple organ systems.

Active maintenance of CD8+ T cell naïvety through regulation of global genome architecture

The differentiation of naïve CD8+ cytotoxic T lymphocytes (CTLs) into effector and memory states results in large scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organisation reflect or underpin these transcriptional programs. We utilised Hi-C to map changes in the spatial organisation of long-range genome contacts within naïve, effector and memory virus-specific CD8+ T cells. We observed that the architecture of the naive CD8+ T cell genome was distinct from effector and memory genome configurations with extensive changes within discrete functional chromatin domains. However, deletion of the BACH2 or SATB1 transcription factors was sufficient to remodel the naïve chromatin architecture and engage transcriptional programs characteristic of differentiated cells. This suggests that the chromatin architecture within naïve CD8+ T cells is preconfigured to undergo autonomous remodelling upon activation, with key transcription factors restraining differentiation by actively enforcing the unique naïve chromatin state.

Kidney Organoids Generated Using an Allelic Series of NPHS2 Point Variants Reveal Distinct Intracellular Podocin Mistrafficking

BACKGROUND

NPHS2 variants are the most common cause of steroid-resistant nephrotic syndrome in children >1 month old. Missense NPHS2 variants were reported to cause mistrafficking of the encoded protein, PODOCIN, but this conclusion was on the basis of overexpression in some nonpodocyte cell lines.

METHODS

We generated a series of human induced pluripotent stem cell (iPSC) lines bearing pathogenic missense variants of NPHS2 , encoding the protein changes p.G92C, p.P118L, p.R138Q, p.R168H, and p.R291W, and control lines. iPSC lines were also generated from a patient with steroid-resistant nephrotic syndrome (p.R168H homozygote) and a healthy heterozygous parent. All lines were differentiated into kidney organoids. Immunofluorescence assessed PODOCIN expression and subcellular localization. Podocytes were transcriptionally profiled and PODOCIN-NEPHRIN interaction interrogated.

RESULTS

All variant lines revealed reduced levels of PODOCIN protein in the absence of reduced transcription. Although wild-type PODOCIN localized to the membrane, distinct variant proteins displayed unique patterns of subcellular protein trafficking, some unreported. P118L and R138Q were preferentially retained in the endoplasmic reticulum (ER); R168H and R291W accumulated in the Golgi. Podocyte profiling demonstrated minimal disease-associated transcriptional change. All variants displayed podocyte-specific apoptosis, which was not linked to ER stress. NEPHRIN-PODOCIN colocalization elucidated the variant-specific effect on NEPHRIN association and hence NEPHRIN trafficking.

CONCLUSIONS

Specific variants of endogenous NPHS2 result in distinct subcellular PODOCIN localization within organoid podocytes. Understanding the effect of each variant on protein levels and localization and the effect on NEPHRIN provides additional insight into the pathobiology of NPHS2 variants.

PODCAST

This article contains a podcast at https://dts.podtrac.com/redirect.mp3/www.asn-online.org/media/podcast/JASN/2023_01_05_JASN2022060707.mp3.

Parallel use of pluripotent human stem cell lung and heart models provide new insights for treatment of SARS-CoV-2

SARS-CoV-2 primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe COVID-19. To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type II (AT2) epithelial cell and cardiac cultures infected with SARS-CoV-2. With CRISPR- Cas9 mediated knock-out of ACE2, we demonstrated that angiotensin converting enzyme 2 (ACE2) was essential for SARS-CoV-2 infection of both cell types but further processing in lung cells required TMPRSS2 while cardiac cells required the endosomal pathway. Host responses were significantly different; transcriptome profiling and phosphoproteomics responses depended strongly on the cell type. We identified several antiviral compounds with distinct antiviral and toxicity profiles in lung AT2 and cardiac cells, highlighting the importance of using several relevant cell types for evaluation of antiviral drugs. Our data provide new insights into rational drug combinations for effective treatment of a virus that affects multiple organ systems.

One-sentence summary

Rational treatment strategies for SARS-CoV-2 derived from human PSC models.

Current and Emerging Trends in Diabetes Care and Education: 2021 National Practice and Workforce Survey

PURPOSE

The purpose of the National Practice Survey is to understand current trends related to the diabetes care and education specialist's integration into the full care team beyond formal diabetes self-management education and support services.

METHODS

The 2021 National Practice Survey (NPS2021) contained 61 questions for all respondents with an additional 56 questions pertaining to specific diabetes care and education segments. An anonymous survey was administered online to respondents who are diabetes care and education specialists or a part of the diabetes care team. Email lists were obtained from the Association of Diabetes Care & Education Specialists (ADCES) and the Certification Board for Diabetes Care and Education (CBDCE). Approximately 39,258 emails were sent, and 3357 were undeliverable, with 3797 surveys completed between February 9 to April 6, 2021, resulting in an 11% response rate. The response rate may have been affected by the COVID-19 public health emergency.

RESULTS

Diabetes care and education specialists represent an interprofessional specialty of nurses, dietitians, physicians, pharmacists, health educators, and others. Many respondents reported holding either certification as a Certified Diabetes Care and Education Specialist (CDCES) or being Board Certified in Advanced Diabetes Management (BC-ADM). In addition, there appears to be a slight increase in those trained as a Lifestyle Coach to provide the National Diabetes Prevention Program (CDC Recognized National DPP) compared to NPS2017. Most respondents reported being Caucasian/White (84%), followed by Hispanic or Latinx (7%) and African American/Black and Asian/Asian American (at 4% each), like in previous surveys. Respondents reported diverse care delivery models, including traditional and nontraditional services, and expanded models of care such as population health/risk stratification models, the Chronic Care Model, Accountable Care Organizations, managed care, and others.

CONCLUSION

The NPS2021 describes DCES workforce opportunities and challenges. Identifying and addressing those that impact the specialty's sustainability, diversity, and growth will guide strategies for the future workforce and their practice settings. Opportunities identified include embracing diabetes community care coordinators for person-centered delivery of care and education services and supporting frontline health care team members to increase competence and expertise in the prevention of type 2 diabetes, diabetes care, and education/support for related chronic diseases. In addition, as health care evolves, it creates opportunities for the DCESs to demonstrate a broader, key role as part of the diabetes care team.

A cis-regulatory-directed pipeline for the identification of genes involved in cardiac development and disease

BACKGROUND

Congenital heart diseases are the major cause of death in newborns, but the genetic etiology of this developmental disorder is not fully known. The conventional approach to identify the disease-causing genes focuses on screening genes that display heart-specific expression during development. However, this approach would have discounted genes that are expressed widely in other tissues but may play critical roles in heart development.

RESULTS

We report an efficient pipeline of genome-wide gene discovery based on the identification of a cardiac-specific cis-regulatory element signature that points to candidate genes involved in heart development and congenital heart disease. With this pipeline, we retrieve 76% of the known cardiac developmental genes and predict 35 novel genes that previously had no known connectivity to heart development. Functional validation of these novel cardiac genes by RNAi-mediated knockdown of the conserved orthologs in Drosophila cardiac tissue reveals that disrupting the activity of 71% of these genes leads to adult mortality. Among these genes, RpL14, RpS24, and Rpn8 are associated with heart phenotypes.

CONCLUSIONS

Our pipeline has enabled the discovery of novel genes with roles in heart development. This workflow, which relies on screening for non-coding cis-regulatory signatures, is amenable for identifying developmental and disease genes for an organ without constraining to genes that are expressed exclusively in the organ of interest.

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast

Most eukaryotic mRNAs accommodate alternative sites of poly(A) addition in the 3’ untranslated region in order to regulate mRNA function. Here, we present a systematic analysis of 3’ end formation factors, which revealed 3’UTR lengthening in response to a loss of the core machinery, whereas a loss of the Sen1 helicase resulted in shorter 3’UTRs. We show that the anti-cancer drug cordycepin, 3’ deoxyadenosine, caused nucleotide accumulation and the usage of distal poly(A) sites. Mycophenolic acid, a drug which reduces GTP levels and impairs RNA polymerase II (RNAP II) transcription elongation, promoted the usage of proximal sites and reversed the effects of cordycepin on alternative polyadenylation. Moreover, cordycepin-mediated usage of distal sites was associated with a permissive chromatin template and was suppressed in the presence of an rpb1 mutation, which slows RNAP II elongation rate. We propose that alternative polyadenylation is governed by temporal coordination of RNAP II transcription and 3’ end processing and controlled by the availability of 3’ end factors, nucleotide levels and chromatin landscape.

The YEATS Domain Histone Crotonylation Readers Control Virulence-Related Biology of a Major Human Pathogen

Identification of multiple histone acylations diversifies transcriptional control by metabolism, but their functions are incompletely defined. Here we report evidence of histone crotonylation in the human fungal pathogen Candida albicans. We define the enzymes that regulate crotonylation and show its dynamic control by environmental signals: carbon sources, the short-chain fatty acids butyrate and crotonate, and cell wall stress. Crotonate regulates stress-responsive transcription and rescues C. albicans from cell wall stress, indicating broad impact on cell biology. The YEATS domain crotonylation readers Taf14 and Yaf9 are required for C. albicans virulence, and Taf14 controls gene expression, stress resistance, and invasive growth via its chromatin reader function. Blocking the Taf14 C terminus with a tag reduced virulence, suggesting that inhibiting Taf14 interactions with chromatin regulators impairs function. Our findings shed light on the regulation of histone crotonylation and the functions of the YEATS proteins in eukaryotic pathogen biology and fungal infections.

Laser arytenoidectomy for bilateral vocal fold palsy in Parkinson's disease

We report a case of laser arytenoidectomy for bilateral abductor palsy of the vocal fold in a patient with Parkinson's disease. Parkinson's disease is known to be a rare cause for bilateral vocal fold palsy and this is the second case reported in the English literature. Majority of the reports to date are in the non-English literature. Tracheostomy has been the classic treatment option offered to these patients. To date no report has been found in the literature about a laser arytenoidectomy being performed in a patient suffering from bilateral vocal fold palsy in Parkinson's disease. We have suggested this option as it improves the quality of life of the individual and avoids the difficulty faced by a Parkinson's patient in managing tracheostomy care due to bradykinesia, rigidity and tremor.

The value of bone scintigraphy in the evaluation of osteoporotic patients with back pain

We evaluated the role of bone scintigraphy in 60 osteoporotic patients with back pain. Thirty-four had scintigraphic evidence of vertebral fracture and were found to have a significantly lower bone density compared to those without fractures (p = 0.01). In only 14 patients was vertebral fracture considered to be the sole cause of pain with 38 having alternative abnormalities, the most common of which was facet joint disease (n = 30). Results of bone scintigraphy influenced a direct change in management in 18 patients and were able to exclude vertebral fracture as a cause of symptoms in 30. In symptomatic osteoporotic patients the bone scan may be helpful in elucidating the etiology of back pain and can impact on patient management.

Availability of cigarettes to minors

Legislation banning the sale of cigarettes to minors is potentially a cost-effective means of reducing smoking rates among adolescents. Such legislation has been in existence in Australia for over 80 years. Two studies examined the retail industry's adherence to the sales ban in two regions of New South Wales in 1990. The first study was a survey of 1,849 12- to 15-year-old adolescents from 12 high schools in New South Wales, providing data on self-reported purchasing of cigarettes from retail outlets by minors. In all, 38 per cent reported having purchased cigarettes illegally. A second study was undertaken to determine the proportion of retail shops which sell cigarettes to apparently underage youth. Two 16-year-olds who looked young for their age attempted to purchase cigarettes from 101 different retail outlets in one region of New South Wales. No challenge about age was made for 70 per cent of purchases, and proof of age was requested on only 15 per cent of occasions. The results suggest that legislation banning sales of cigarettes to minors requires strong enforcement procedures to be effective.